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Rhizosphere immunity: targeting the underground for sustainable plant health management

Zhong WEI, Ville-Petri FRIMAN, Thomas POMMIER, Stefan GEISEN, Alexandre JOUSSET, Qirong SHEN

《农业科学与工程前沿（英文）》 2020年 第7卷 第3期   页码 317-328 doi: 10.15302/J-FASE-2020346

摘要：

Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between plants, microbiota and the surrounding soil matrix. These interactions can potentially extend the innate plant immune system to a point where the rhizosphere immunity can fulfil all four core functions of a full immune system: pathogen prevention, recognition, response and homeostasis. We suggest that considering plant health from a meta-organism perspective will help in developing multidisciplinary pathogen management strategies that focus on steering the whole plant-microbe-soil networks instead of individual components. This might be achieved by bringing together the latest discoveries in phytopathology, microbiome research, soil science and agronomy to pave the way toward more sustainable and productive agriculture.

关键词： rhizosphere     soil microbiome     plant immunity     microbial ecology     plant health     soilborne pathogens    

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IMPACTS OF CLIMATE CHANGE ON CROP PRODUCTION, PESTS AND PATHOGENS OF WHEAT AND RICE

《农业科学与工程前沿（英文）》 2022年 第9卷 第1期   页码 4-18 doi: 10.15302/J-FASE-2021432

摘要：

Ongoing climate change is expected to have impacts on crops, insect pests, and plant pathogens and poses considerable threats to sustainable food security. Existing reviews have summarized impacts of a changing climate on agriculture, but the majority of these are presented from an ecological point of view, and scant information is available on specific species in agricultural applications. This paper provides an overview of impacts of climate change on two staple crops, wheat and rice. First, the direct effects of climate change on crop growth, yield formation, and geographic distribution of wheat and rice are reviewed. Then, the effects of climate change on pests and pathogens related with wheat and rice, and their interactions with the crops are summarized. Finally, potential management strategies to mitigate the direct impacts of climate change on crops, and the indirect impacts on crops through pests and pathogens are outlined. The present overview aims to aid agriculture practitioners and researchers who are interested in wheat and rice to better understand climate change related impacts on the target species.

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

《医学前沿（英文）》 2022年 第16卷 第2期   页码 251-262 doi: 10.1007/s11684-021-0915-9

摘要： Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic

《环境科学与工程前沿（英文）》 2022年 第16卷 第8期 doi: 10.1007/s11783-022-1521-z

摘要：

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

关键词： UV/chlorine process     Pathogen     Antibiotic resistance genes     High-throughput qPCR     Reclaimed water    

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., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

《农业科学与工程前沿（英文）》 2018年 第5卷 第3期   页码 330-339 doi: 10.15302/J-FASE-2018208

摘要：

Cronobacter spp. (formerly Enterobacter sakazakii) are special foodborne pathogens. Cronobacter infection can cause necrotizing enterocolitis, sepsis and meningitis in all age groups, especially neonates and infants, with a high fatality of up to 80%, although the infection is rare. Outbreaks of Cronobacter infection are epidemiologically proven to be associated with contaminated powdered infant formula (PIF). Cronobacter spp. can resist dry environments and survive for a long period in food with low water activity. Therefore, Cronobacter spp. have become serious pathogens of neonates and infants, as well as in the dairy industry. In this review, we present the taxonomy, pathogenesis, resistance, detection and control of Cronobacter spp.

关键词： Cronobacter spp.     desiccation resistance     pathogen control     pathogen detection     powdered infant formula    

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Mitigating microbiological risks of potential pathogens carrying antibiotic resistance genes and virulence

《环境科学与工程前沿（英文）》 2023年 第17卷 第7期 doi: 10.1007/s11783-023-1682-4

摘要：

● Abundance of MAGs carrying ARG-VF pairs unchanged in rivers after WWTP upgrade.

关键词： Wastewater treatment plant upgrade     Antibiotic resistance genes (ARGs)     Virulence factors (VFs)     Gene co-occurrence     Genome-centric analysis    

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Hydrothermal carbonization of livestock mortality for the reduction of pathogens and microbially-derived

Thomas F. Ducey, Jessica C. Collins, Kyoung S. Ro, Bryan L. Woodbury, D. Dee Griffin

《环境科学与工程前沿（英文）》 2017年 第11卷 第3期 doi: 10.1007/s11783-017-0930-x

摘要： Hydrothermal carbonization (HTC), utilizing high temperature and pressure, has the potential to treat agricultural waste via inactivating pathogens, antibiotic resistance genes (ARG), and contaminants of emerging concern (CEC) in a environmental and economical manner. Livestock mortality is one facet of agricultural waste that can pose a threat to the surrounding environment. While several methods are utilized to treat livestock mortality, there remains a paucity of data on the elimination of microbially-derived DNA in these treatment practices. This DNA, most notably ARGs, if it survives treatment can be reintroduced in agricultural environments where it could potentially be passed to pathogens, posing a risk to animal and human populations. HTC treatments have been successfully utilized for the treatment of CECs, however very little is understood on how ARGs survive HTC treatment. This study aims to fill this knowledge gap by examining the survivability of microbially-derived DNA in the HTC treatment of livestock mortality. We examined three treatment temperatures (100°C, 150°C, and 200°C) at autogenic pressures at three treatment times (30, 60, and 240 min). We examined the amplification of a plasmid-borne reporter gene carried by DH10B introduced to both beef bone and tissue. Results indicate that while all three temperatures, at all treatment times, were suitable for complete pathogen kill, only temperatures of 150°C and 200°C were sufficient for eliminating microbial DNA. These results serve as the basis for future potential HTC treatment recommendations for livestock mortality when considering the elimination of pathogens and ARGs.

关键词： High-temperature carbonization     Microbial DNA     Livestock mortality    

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Association between heavy metals and antibiotic-resistant human pathogens in environmental reservoirs

Christine C. Nguyen, Cody N. Hugie, Molly L. Kile, Tala Navab-Daneshmand

《环境科学与工程前沿（英文）》 2019年 第13卷 第3期 doi: 10.1007/s11783-019-1129-0

摘要：

Heavy metals can act as co-selecting agents and promote antibiotic resistance.

Most frequent resistances to heavy metals are observed for zinc and cadmium.

P. aeruginosa and E. coli are commonly resistant to heavy metals and antibiotics.

Heavy metals proliferate antibiotic resistance through co- and cross-resistance.

Heavy metal and antibiotic resistances are common near anthropogenic activities.

关键词： Zinc     Cadmium     Copper     Lead     E. coli     P. aeruginosa    

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植物病原菌致病策略——利用效应子挟持寄主内质网

景茂峰, 王源超

《工程（英文）》 2020年 第6卷 第5期   页码 500-504 doi: 10.1016/j.eng.2020.03.003

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Antibodies Targeting a Conserved Surface Polysaccharide Are Protective Against a Wide Range of Microbial Pathogens

Xi Lu,Guoqing Li,Jing Pang,Xinyi Yang,Colette Cywes-Bentley,Xuefu You,Gerald B. Pier,

《工程（英文）》 doi: 10.1016/j.eng.2023.09.012

摘要： The β-1–6-linked poly-N-acetylglucosamine (PNAG) polymer is a conserved surface polysaccharide produced by many bacteria, fungi, and protozoan (and even filarial) parasites. This wide-ranging expression makes PNAG an attractive target for vaccine development, as it potentially encompasses a broad range of microorganisms. Significant progress has been made in discovering important properties of the biology of PNAG expression in recent years. The molecular characterization and regulation of operons for the production of PNAG biosynthetic proteins and enzymes have been studied in many bacteria. In addition, the physiological function of PNAG has been further elucidated. PNAG-based vaccines and PNAG-targeting antibodies have shown great efficacy in preclinical research. Furthermore, clinical tests for both vaccines and antibodies have been carried out in humans and economically important animals, and the results are promising. Although it is not destined to be a smooth road, we are optimistic about new vaccines and immunotherapeutics targeting PNAG becoming validated and eventually licensed for clinical use against multiple infectious agents.

关键词： Poly-     N     -acetylglucosamine     Conjugate vaccine     Monoclonal antibody    

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species associated with eucalypt diseases in southern China

Shuaifei CHEN, Qianli LIU, Guoqing LI, Michael J. WINGFIELD

《农业科学与工程前沿（英文）》 2017年 第4卷 第4期   页码 433-447 doi: 10.15302/J-FASE-2017173

摘要： The genus includes several important pathogens of species of and , mainly causing leaf and shoot blight. Recently, extensive shoot and leaf dieback and stem cankers suspected to be diseases have been found on young trees in Guangdong and Hainan Provinces. The occurrence of species and their association with eucalypt hosts within China needs to be investigated for tree diseases management. The isolates from the diseased samples were identified based on their morphological structures and phylogenetic analyses with DNA sequence data for the internal transcribed spacer region and large ribosome subunit RNA of the nuclear rDNA. This work revealed that three species of were present: from , from , both isolated from young eucalypt leaves and shoots in Guangdong Province, and , which was isolated from stem cankers of at four different sites across Guangdong and Hainan Provinces. These results confirmed that agents were associated with the diseases occurring on eucalypt hosts in South China. This is the first report of in Asia and the first report of in China on trees.

关键词： Corymbia     Eucalyptus     forest pathogens     plantations     Myrtaceae    

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海水养殖细菌性病害检测方法研究进展

肖婧凡,王玥,张元兴,雷霁霖

《中国工程科学》 2014年 第16卷 第9期   页码 10-15

摘要：

随着我国水产养殖业的不断发展，各种病害问题日益突出。细菌性病害在所有病害中占到相当大的比例，因此其检测方法的开发在水产养殖病害发现、防治、无公害水产品生产及卫生质量检验中均具有重要意义。本文对近年来国内外主要海水养殖细菌性病害检测方法的研究情况进行综述，介绍了主要细菌性病害的各种检测方法的原理、应用及其研究进展，为我国今后建立水产养殖细菌性病害检测方法标准及推动相应检测产品的商品化提供参考。

关键词： 水产养殖     细菌性病害     检测方法    

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鲆鲽类主要病原菌抗血清的制备及应用

甘玲玲,王蔚芳,高淳仁,雷霁霖

《中国工程科学》 2014年 第16卷 第9期   页码 21-25

摘要：

用甲醛灭活8 种鲆鲽类主要病原菌，鳗弧菌(Vibrio anguillarum)、创伤弧菌(Vibrio vulnificus)、哈维弧菌(Vibrio harveyi)、溶藻弧菌(Vibrio alginolyticus)、嗜水气单胞菌(Aeromonas hydrophila)、豚鼠气单胞菌(Aeromonas caviae)、迟缓爱德华菌(Edwardsiella tarda)、鮰爱德华菌(Edwardsiella ictaluri)，制备成灭活疫苗后肌肉注射大菱鲆获得各病原菌抗血清。结果显示，抗鳗弧菌血清、抗哈维弧菌血清、抗豚鼠气单胞菌血清、抗鮰爱德华菌效价为1:6 400，抗创伤弧菌血清、抗溶藻弧菌血清、抗嗜水气单胞菌血清效价为1:12 800，抗迟缓爱德华菌血清效价为1:102 400。应用ELISA分析各抗血清与8 种病原菌及迟缓爱德华菌蛋白的免疫交叉反应，结果显示，各病原菌与其本身的抗血清反应最为强烈，而与其他抗血清间有程度不等的交叉反应；菌蛋白与其相应的菌抗血清反应最为强烈，与其他病原菌抗血清反应较弱。本研究所制备的病原菌抗血清效价较高，且具有特异性，可应用于鲆鲽类病原菌的检测。

关键词： 鲆鲽类     疫苗     抗血清     病原菌    

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技术发展现状——为什么施工中会出现返工？返工会造成什么后果？怎样才能减少返工？ Review

Peter E.D. Love, Jane Matthews, Michael C.P. Sing, Stuart R. Porter, Weili Fang

《工程（英文）》 2022年 第18卷 第11期   页码 246-258 doi: 10.1016/j.eng.2022.05.010

摘要：

已有大量研究对施工中的返工问题进行了研究，但解决返工问题的成效有限，仍然困扰着施工进程，这对项目的绩效产生不利影响。几乎所有返工研究都侧重于确定其近端或根本原因，因此忽略了导致返工的条件。本文借鉴了之前的实证研究，对这一空白进行了研究，以提供一个急需的理论框架，从而更好地理解返工原因、返工后果以及如何在施工期间减少返工。从审查中得出的理论框架使施工组织认识到，减少返工应首先建立一套差错管理文化，包括真正的领导力、心理安全、差错管理导向和复原力。本研究认为，一旦在施工组织及其项目中建立了差错管理文化，施工组织就能更好地认识用于解决返工问题的方法、工具和技术的益处，如精益生产®和建筑信息模型。本文还为未来研究提供了方向，并确定了对实践的意义，以便能够在施工中减少返工。

关键词： 施工     差错     差错管理文化     病原体     返工     违规    

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标题 作者 时间 类型 操作

Rhizosphere immunity: targeting the underground for sustainable plant health management

Zhong WEI, Ville-Petri FRIMAN, Thomas POMMIER, Stefan GEISEN, Alexandre JOUSSET, Qirong SHEN

期刊论文

IMPACTS OF CLIMATE CHANGE ON CROP PRODUCTION, PESTS AND PATHOGENS OF WHEAT AND RICE

期刊论文

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

期刊论文

Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic

期刊论文

., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

期刊论文

Mitigating microbiological risks of potential pathogens carrying antibiotic resistance genes and virulence

期刊论文

Hydrothermal carbonization of livestock mortality for the reduction of pathogens and microbially-derived

Thomas F. Ducey, Jessica C. Collins, Kyoung S. Ro, Bryan L. Woodbury, D. Dee Griffin

期刊论文

Association between heavy metals and antibiotic-resistant human pathogens in environmental reservoirs

Christine C. Nguyen, Cody N. Hugie, Molly L. Kile, Tala Navab-Daneshmand

期刊论文

植物病原菌致病策略——利用效应子挟持寄主内质网

景茂峰, 王源超

期刊论文

Antibodies Targeting a Conserved Surface Polysaccharide Are Protective Against a Wide Range of Microbial Pathogens

Xi Lu,Guoqing Li,Jing Pang,Xinyi Yang,Colette Cywes-Bentley,Xuefu You,Gerald B. Pier,

期刊论文

species associated with eucalypt diseases in southern China

Shuaifei CHEN, Qianli LIU, Guoqing LI, Michael J. WINGFIELD

期刊论文

海水养殖细菌性病害检测方法研究进展

肖婧凡,王玥,张元兴,雷霁霖

期刊论文

鲆鲽类主要病原菌抗血清的制备及应用

甘玲玲,王蔚芳,高淳仁,雷霁霖

期刊论文

技术发展现状——为什么施工中会出现返工？返工会造成什么后果？怎样才能减少返工？

Peter E.D. Love, Jane Matthews, Michael C.P. Sing, Stuart R. Porter, Weili Fang

期刊论文

韩军：动物重要病原的免疫抑制与逃逸机制前沿进展解读（2022年12月15日）

2022年12月22日

会议视频